Intra-patient HPV genetic variation

Summary & main findings

A unique next-generation sequencing protocol, TaME-seq, was developed for analysis of HPV genomic variation and integration. The results show that the overall intra-host HPV genomic variability is higher than previously assumed, with a high number of HPV genome variants found in all samples from early infections to cancer. A noticeable part of the mutations in HPV16, which is the most carcinogenic HPV type, was associated with the APOBEC3-enzyme that is suggested to be involved in viral clearance. The findings revealed integration sites that located both in previously reported and novel genomic sites. A large number of integrations was observed in or close to human cancer-related genes, which could be an indication of a more aggressive infection.

The TaME-seq method could potentially be a valuable method for assessing the risk of developing cervical cancer. An additional HPV screening test would enable more personalised follow-up, improving detection of lesions with higher risk of progression and reducing unnecessary follow-up and treatment of women with minimal risk of developing high-grade lesions or cancer.

Background

HPV is the etiological agent of cervical cancer and HPV DNA testing is used in cervical cancer screening programs. The main challenge, however is the low clinical specificity of existing HPV tests. This project aims therefore to test if the level of sequence variation in HPV DNA from cervical cells can be used as a marker for cancer progression, and if cancer risk can be stratified down to the level of genetic variants of HPV types.                                                

Methods

Two next-generation sequencing (NGS) based methods, developed in collaboration with FIMM, are used for genotyping HPV types, analyzing genetic diversity in the whole HPV genome and determination of integration sites in the human genome. Data analysis pipelines to process the sequence data are established at CRN. Preliminary data, that was sequenced at Ahus and processed at CRN, shows that the level of intra-patient HPV genetic variation is much higher than expected.

Preparation of clinical trials of a more clinically specific HPV test will be the output if findings in this project support the hypotheses. The improvement of HPV diagnostics will alleviate anxiety in HPV positive women in screening, shorten follow-up and ultimately prevent cervical cancer from developing.